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Search results for the GEO ID: GSE23002

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GSM567573

GPL1261

B16F1 melanoma tumor grown in TNFR 1, 2 -/- mouse, untreated, technical replicate 1

Untreated B16F1 melanoma tumor grown in TNFR 1, 2 -/- mouse

tissue: whole melanoma tumor host strain: C57BL/6 host genotype: TNFR 1, 2 -/- treatment: untreated

Gene expression data from untreated B16F1 melanoma tumor grown in TNFR 1, 2 -/- mouse.

Sample_geo_accession	GSM567573
Sample_status	Public on Jul 20 2010
Sample_submission_date	Jul 19 2010
Sample_last_update_date	Jul 28 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	For radiation exposure, mice were restrained in plexiglass cages and all but the tumor-bearing hind limb was shielded with lead. A single dose of 20 Gray (Gy) was delivered using a Phillips orthovoltage X-ray generator operating at 250 kV and 15 mA.
Sample_growth_protocol_ch1	B16F1 murine melanoma cells were obtained from the American Type Culture Collection (Manassas, VA) and cultured in RPMI 1640 culture medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (Atlanta Biologicals, Lawrenceville, GA), 100 units/ml penicillin and 100 mg/ml streptomycin (Invitrogen, Carlsbad, CA). Cell cultures were maintained at 37 deg C in a humidified environment containing 5% CO2. C57BL/6-NCr (C57BL/6 wild-type) mice were obtained from FCRI-Taconic (Germantown, NY). B6;129S-Tnfrsf1a[tm1Imx] Tnfrsf1b[tm1Imx]/J (TNFR1,2 -/-) breeding pairs were obtained from Jackson Laboratories (Bar Harbor, ME). Mice were 8-12 weeks of age when experimentation began. B16F1 cells (2x10^6 cells in 100 μl of phosphate-buffered saline) were injected subcutaneously into the right hind limbs of five to seven C57BL/6 and TNFR1,2 -/- mice. Tumor volume was determined by direct measurement with calipers and calculated by using the formula (length x width x depth/2). Tumors were permitted to grow to a volume of 268-478 mm3 after which mice were divided into treatment groups with equal mean tumor volumes.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	At the conclusion of each experiment, the animals were euthanized using CO2 followed by cervical dislocation in accordance with institutional guidelines. Tumors were excised five hours following treatment and snap frozen in liquid nitrogen. TRIzol extraction of total RNA was performed according to the manufacturer's instructions. Samples were pooled based on total RNA and analyzed in duplicate.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix GeneChip® Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Agilent GeneArray Scanner.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 800.
Sample_platform_id	GPL1261
Sample_contact_name	Sean,Pravin,Pitroda
Sample_contact_email	spitroda@uchicago.edu
Sample_contact_department	Radiation and Cellular Oncology
Sample_contact_institute	The University of Chicago
Sample_contact_address	5841 South Maryland Avenue, MC 1105
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60637
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM567nnn/GSM567573/suppl/GSM567573.CEL.gz
Sample_series_id	GSE23002
Sample_data_row_count	45101

GSM567574

GPL1261

B16F1 melanoma tumor grown in TNFR 1, 2 -/- mouse, untreated, technical replicate 2

Untreated B16F1 melanoma tumor grown in TNFR 1, 2 -/- mouse

tissue: whole melanoma tumor host strain: C57BL/6 host genotype: TNFR 1, 2 -/- treatment: untreated

Gene expression data from untreated B16F1 melanoma tumor grown in TNFR 1, 2 -/- mouse.

Sample_geo_accession	GSM567574
Sample_status	Public on Jul 20 2010
Sample_submission_date	Jul 19 2010
Sample_last_update_date	Jul 28 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	For radiation exposure, mice were restrained in plexiglass cages and all but the tumor-bearing hind limb was shielded with lead. A single dose of 20 Gray (Gy) was delivered using a Phillips orthovoltage X-ray generator operating at 250 kV and 15 mA.
Sample_growth_protocol_ch1	B16F1 murine melanoma cells were obtained from the American Type Culture Collection (Manassas, VA) and cultured in RPMI 1640 culture medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (Atlanta Biologicals, Lawrenceville, GA), 100 units/ml penicillin and 100 mg/ml streptomycin (Invitrogen, Carlsbad, CA). Cell cultures were maintained at 37 deg C in a humidified environment containing 5% CO2. C57BL/6-NCr (C57BL/6 wild-type) mice were obtained from FCRI-Taconic (Germantown, NY). B6;129S-Tnfrsf1a[tm1Imx] Tnfrsf1b[tm1Imx]/J (TNFR1,2 -/-) breeding pairs were obtained from Jackson Laboratories (Bar Harbor, ME). Mice were 8-12 weeks of age when experimentation began. B16F1 cells (2x10^6 cells in 100 μl of phosphate-buffered saline) were injected subcutaneously into the right hind limbs of five to seven C57BL/6 and TNFR1,2 -/- mice. Tumor volume was determined by direct measurement with calipers and calculated by using the formula (length x width x depth/2). Tumors were permitted to grow to a volume of 268-478 mm3 after which mice were divided into treatment groups with equal mean tumor volumes.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	At the conclusion of each experiment, the animals were euthanized using CO2 followed by cervical dislocation in accordance with institutional guidelines. Tumors were excised five hours following treatment and snap frozen in liquid nitrogen. TRIzol extraction of total RNA was performed according to the manufacturer's instructions. Samples were pooled based on total RNA and analyzed in duplicate.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix GeneChip® Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Agilent GeneArray Scanner.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 800.
Sample_platform_id	GPL1261
Sample_contact_name	Sean,Pravin,Pitroda
Sample_contact_email	spitroda@uchicago.edu
Sample_contact_department	Radiation and Cellular Oncology
Sample_contact_institute	The University of Chicago
Sample_contact_address	5841 South Maryland Avenue, MC 1105
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60637
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM567nnn/GSM567574/suppl/GSM567574.CEL.gz
Sample_series_id	GSE23002
Sample_data_row_count	45101

GSM567575

GPL1261

B16F1 melanoma tumor grown in TNFR 1, 2 -/- mouse, irradiated, technical replicate 1

Irradiated B16F1 melanoma tumor grown in TNFR 1, 2 -/- mouse

tissue: whole melanoma tumor host strain: C57BL/6 host genotype: TNFR 1, 2 -/- treatment: irradiated

Gene expression data from irradiated B16F1 melanoma tumor grown in TNFR 1, 2 -/- mouse.

Sample_geo_accession	GSM567575
Sample_status	Public on Jul 20 2010
Sample_submission_date	Jul 19 2010
Sample_last_update_date	Jul 28 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	For radiation exposure, mice were restrained in plexiglass cages and all but the tumor-bearing hind limb was shielded with lead. A single dose of 20 Gray (Gy) was delivered using a Phillips orthovoltage X-ray generator operating at 250 kV and 15 mA.
Sample_growth_protocol_ch1	B16F1 murine melanoma cells were obtained from the American Type Culture Collection (Manassas, VA) and cultured in RPMI 1640 culture medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (Atlanta Biologicals, Lawrenceville, GA), 100 units/ml penicillin and 100 mg/ml streptomycin (Invitrogen, Carlsbad, CA). Cell cultures were maintained at 37 deg C in a humidified environment containing 5% CO2. C57BL/6-NCr (C57BL/6 wild-type) mice were obtained from FCRI-Taconic (Germantown, NY). B6;129S-Tnfrsf1a[tm1Imx] Tnfrsf1b[tm1Imx]/J (TNFR1,2 -/-) breeding pairs were obtained from Jackson Laboratories (Bar Harbor, ME). Mice were 8-12 weeks of age when experimentation began. B16F1 cells (2x10^6 cells in 100 μl of phosphate-buffered saline) were injected subcutaneously into the right hind limbs of five to seven C57BL/6 and TNFR1,2 -/- mice. Tumor volume was determined by direct measurement with calipers and calculated by using the formula (length x width x depth/2). Tumors were permitted to grow to a volume of 268-478 mm3 after which mice were divided into treatment groups with equal mean tumor volumes.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	At the conclusion of each experiment, the animals were euthanized using CO2 followed by cervical dislocation in accordance with institutional guidelines. Tumors were excised five hours following treatment and snap frozen in liquid nitrogen. TRIzol extraction of total RNA was performed according to the manufacturer's instructions. Samples were pooled based on total RNA and analyzed in duplicate.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix GeneChip® Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Agilent GeneArray Scanner.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 800.
Sample_platform_id	GPL1261
Sample_contact_name	Sean,Pravin,Pitroda
Sample_contact_email	spitroda@uchicago.edu
Sample_contact_department	Radiation and Cellular Oncology
Sample_contact_institute	The University of Chicago
Sample_contact_address	5841 South Maryland Avenue, MC 1105
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60637
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM567nnn/GSM567575/suppl/GSM567575.CEL.gz
Sample_series_id	GSE23002
Sample_data_row_count	45101

GSM567576

GPL1261

B16F1 melanoma tumor grown in TNFR 1, 2 -/- mouse, irradiated, technical replicate 2

Irradiated B16F1 melanoma tumor grown in TNFR 1, 2 -/- mouse

tissue: whole melanoma tumor host strain: C57BL/6 host genotype: TNFR 1, 2 -/- treatment: irradiated

Gene expression data from irradiated B16F1 melanoma tumor grown in TNFR 1, 2 -/- mouse.

Sample_geo_accession	GSM567576
Sample_status	Public on Jul 20 2010
Sample_submission_date	Jul 19 2010
Sample_last_update_date	Jul 28 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	For radiation exposure, mice were restrained in plexiglass cages and all but the tumor-bearing hind limb was shielded with lead. A single dose of 20 Gray (Gy) was delivered using a Phillips orthovoltage X-ray generator operating at 250 kV and 15 mA.
Sample_growth_protocol_ch1	B16F1 murine melanoma cells were obtained from the American Type Culture Collection (Manassas, VA) and cultured in RPMI 1640 culture medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (Atlanta Biologicals, Lawrenceville, GA), 100 units/ml penicillin and 100 mg/ml streptomycin (Invitrogen, Carlsbad, CA). Cell cultures were maintained at 37 deg C in a humidified environment containing 5% CO2. C57BL/6-NCr (C57BL/6 wild-type) mice were obtained from FCRI-Taconic (Germantown, NY). B6;129S-Tnfrsf1a[tm1Imx] Tnfrsf1b[tm1Imx]/J (TNFR1,2 -/-) breeding pairs were obtained from Jackson Laboratories (Bar Harbor, ME). Mice were 8-12 weeks of age when experimentation began. B16F1 cells (2x10^6 cells in 100 μl of phosphate-buffered saline) were injected subcutaneously into the right hind limbs of five to seven C57BL/6 and TNFR1,2 -/- mice. Tumor volume was determined by direct measurement with calipers and calculated by using the formula (length x width x depth/2). Tumors were permitted to grow to a volume of 268-478 mm3 after which mice were divided into treatment groups with equal mean tumor volumes.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	At the conclusion of each experiment, the animals were euthanized using CO2 followed by cervical dislocation in accordance with institutional guidelines. Tumors were excised five hours following treatment and snap frozen in liquid nitrogen. TRIzol extraction of total RNA was performed according to the manufacturer's instructions. Samples were pooled based on total RNA and analyzed in duplicate.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix GeneChip® Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Agilent GeneArray Scanner.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 800.
Sample_platform_id	GPL1261
Sample_contact_name	Sean,Pravin,Pitroda
Sample_contact_email	spitroda@uchicago.edu
Sample_contact_department	Radiation and Cellular Oncology
Sample_contact_institute	The University of Chicago
Sample_contact_address	5841 South Maryland Avenue, MC 1105
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60637
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM567nnn/GSM567576/suppl/GSM567576.CEL.gz
Sample_series_id	GSE23002
Sample_data_row_count	45101

GSM567577

GPL1261

B16F1 melanoma tumor grown in C57BL/6 wild-type mouse, untreated, technical replicate 1

Untreated B16F1 melanoma tumor grown in C57BL/6 wild-type mouse

tissue: whole melanoma tumor host strain: C57BL/6 host genotype: wild-type treatment: untreated

Gene expression data from untreated B16F1 melanoma tumor grown in C57BL/6 wild-type mouse.

Sample_geo_accession	GSM567577
Sample_status	Public on Jul 20 2010
Sample_submission_date	Jul 19 2010
Sample_last_update_date	Jul 28 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	For radiation exposure, mice were restrained in plexiglass cages and all but the tumor-bearing hind limb was shielded with lead. A single dose of 20 Gray (Gy) was delivered using a Phillips orthovoltage X-ray generator operating at 250 kV and 15 mA.
Sample_growth_protocol_ch1	B16F1 murine melanoma cells were obtained from the American Type Culture Collection (Manassas, VA) and cultured in RPMI 1640 culture medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (Atlanta Biologicals, Lawrenceville, GA), 100 units/ml penicillin and 100 mg/ml streptomycin (Invitrogen, Carlsbad, CA). Cell cultures were maintained at 37 deg C in a humidified environment containing 5% CO2. C57BL/6-NCr (C57BL/6 wild-type) mice were obtained from FCRI-Taconic (Germantown, NY). B6;129S-Tnfrsf1a[tm1Imx] Tnfrsf1b[tm1Imx]/J (TNFR1,2 -/-) breeding pairs were obtained from Jackson Laboratories (Bar Harbor, ME). Mice were 8-12 weeks of age when experimentation began. B16F1 cells (2x10^6 cells in 100 μl of phosphate-buffered saline) were injected subcutaneously into the right hind limbs of five to seven C57BL/6 and TNFR1,2 -/- mice. Tumor volume was determined by direct measurement with calipers and calculated by using the formula (length x width x depth/2). Tumors were permitted to grow to a volume of 268-478 mm3 after which mice were divided into treatment groups with equal mean tumor volumes.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	At the conclusion of each experiment, the animals were euthanized using CO2 followed by cervical dislocation in accordance with institutional guidelines. Tumors were excised five hours following treatment and snap frozen in liquid nitrogen. TRIzol extraction of total RNA was performed according to the manufacturer's instructions. Samples were pooled based on total RNA and analyzed in duplicate.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix GeneChip® Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Agilent GeneArray Scanner.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 800.
Sample_platform_id	GPL1261
Sample_contact_name	Sean,Pravin,Pitroda
Sample_contact_email	spitroda@uchicago.edu
Sample_contact_department	Radiation and Cellular Oncology
Sample_contact_institute	The University of Chicago
Sample_contact_address	5841 South Maryland Avenue, MC 1105
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60637
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM567nnn/GSM567577/suppl/GSM567577.CEL.gz
Sample_series_id	GSE23002
Sample_data_row_count	45101

GSM567578

GPL1261

B16F1 melanoma tumor grown in C57BL/6 wild-type mouse, untreated, technical replicate 2

Untreated B16F1 melanoma tumor grown in C57BL/6 wild-type mouse

tissue: whole melanoma tumor host strain: C57BL/6 host genotype: wild-type treatment: untreated

Gene expression data from untreated B16F1 melanoma tumor grown in C57BL/6 wild-type mouse.

Sample_geo_accession	GSM567578
Sample_status	Public on Jul 20 2010
Sample_submission_date	Jul 19 2010
Sample_last_update_date	Jul 28 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	For radiation exposure, mice were restrained in plexiglass cages and all but the tumor-bearing hind limb was shielded with lead. A single dose of 20 Gray (Gy) was delivered using a Phillips orthovoltage X-ray generator operating at 250 kV and 15 mA.
Sample_growth_protocol_ch1	B16F1 murine melanoma cells were obtained from the American Type Culture Collection (Manassas, VA) and cultured in RPMI 1640 culture medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (Atlanta Biologicals, Lawrenceville, GA), 100 units/ml penicillin and 100 mg/ml streptomycin (Invitrogen, Carlsbad, CA). Cell cultures were maintained at 37 deg C in a humidified environment containing 5% CO2. C57BL/6-NCr (C57BL/6 wild-type) mice were obtained from FCRI-Taconic (Germantown, NY). B6;129S-Tnfrsf1a[tm1Imx] Tnfrsf1b[tm1Imx]/J (TNFR1,2 -/-) breeding pairs were obtained from Jackson Laboratories (Bar Harbor, ME). Mice were 8-12 weeks of age when experimentation began. B16F1 cells (2x10^6 cells in 100 μl of phosphate-buffered saline) were injected subcutaneously into the right hind limbs of five to seven C57BL/6 and TNFR1,2 -/- mice. Tumor volume was determined by direct measurement with calipers and calculated by using the formula (length x width x depth/2). Tumors were permitted to grow to a volume of 268-478 mm3 after which mice were divided into treatment groups with equal mean tumor volumes.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	At the conclusion of each experiment, the animals were euthanized using CO2 followed by cervical dislocation in accordance with institutional guidelines. Tumors were excised five hours following treatment and snap frozen in liquid nitrogen. TRIzol extraction of total RNA was performed according to the manufacturer's instructions. Samples were pooled based on total RNA and analyzed in duplicate.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix GeneChip® Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Agilent GeneArray Scanner.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 800.
Sample_platform_id	GPL1261
Sample_contact_name	Sean,Pravin,Pitroda
Sample_contact_email	spitroda@uchicago.edu
Sample_contact_department	Radiation and Cellular Oncology
Sample_contact_institute	The University of Chicago
Sample_contact_address	5841 South Maryland Avenue, MC 1105
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60637
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM567nnn/GSM567578/suppl/GSM567578.CEL.gz
Sample_series_id	GSE23002
Sample_data_row_count	45101

GSM567579

GPL1261

B16F1 melanoma tumor grown in C57BL/6 wild-type mouse, irradiated, technical replicate 1

Irradiated B16F1 melanoma tumor grown in C57BL/6 wild-type mouse

tissue: whole melanoma tumor host strain: C57BL/6 host genotype: wild-type treatment: irradiated

Gene expression data from irradiated B16F1 melanoma tumor grown in C57BL/6 wild-type mouse.

Sample_geo_accession	GSM567579
Sample_status	Public on Jul 20 2010
Sample_submission_date	Jul 19 2010
Sample_last_update_date	Jul 28 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	For radiation exposure, mice were restrained in plexiglass cages and all but the tumor-bearing hind limb was shielded with lead. A single dose of 20 Gray (Gy) was delivered using a Phillips orthovoltage X-ray generator operating at 250 kV and 15 mA.
Sample_growth_protocol_ch1	B16F1 murine melanoma cells were obtained from the American Type Culture Collection (Manassas, VA) and cultured in RPMI 1640 culture medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (Atlanta Biologicals, Lawrenceville, GA), 100 units/ml penicillin and 100 mg/ml streptomycin (Invitrogen, Carlsbad, CA). Cell cultures were maintained at 37 deg C in a humidified environment containing 5% CO2. C57BL/6-NCr (C57BL/6 wild-type) mice were obtained from FCRI-Taconic (Germantown, NY). B6;129S-Tnfrsf1a[tm1Imx] Tnfrsf1b[tm1Imx]/J (TNFR1,2 -/-) breeding pairs were obtained from Jackson Laboratories (Bar Harbor, ME). Mice were 8-12 weeks of age when experimentation began. B16F1 cells (2x10^6 cells in 100 μl of phosphate-buffered saline) were injected subcutaneously into the right hind limbs of five to seven C57BL/6 and TNFR1,2 -/- mice. Tumor volume was determined by direct measurement with calipers and calculated by using the formula (length x width x depth/2). Tumors were permitted to grow to a volume of 268-478 mm3 after which mice were divided into treatment groups with equal mean tumor volumes.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	At the conclusion of each experiment, the animals were euthanized using CO2 followed by cervical dislocation in accordance with institutional guidelines. Tumors were excised five hours following treatment and snap frozen in liquid nitrogen. TRIzol extraction of total RNA was performed according to the manufacturer's instructions. Samples were pooled based on total RNA and analyzed in duplicate.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix GeneChip® Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Agilent GeneArray Scanner.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 800.
Sample_platform_id	GPL1261
Sample_contact_name	Sean,Pravin,Pitroda
Sample_contact_email	spitroda@uchicago.edu
Sample_contact_department	Radiation and Cellular Oncology
Sample_contact_institute	The University of Chicago
Sample_contact_address	5841 South Maryland Avenue, MC 1105
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60637
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM567nnn/GSM567579/suppl/GSM567579.CEL.gz
Sample_series_id	GSE23002
Sample_data_row_count	45101

GSM567580

GPL1261

B16F1 melanoma tumor grown in C57BL/6 wild-type mouse, irradiated, technical replicate 2

Irradiated B16F1 melanoma tumor grown in C57BL/6 wild-type mouse

tissue: whole melanoma tumor host strain: C57BL/6 host genotype: wild-type treatment: irradiated

Gene expression data from irradiated B16F1 melanoma tumor grown in C57BL/6 wild-type mouse.

Sample_geo_accession	GSM567580
Sample_status	Public on Jul 20 2010
Sample_submission_date	Jul 19 2010
Sample_last_update_date	Jul 28 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	For radiation exposure, mice were restrained in plexiglass cages and all but the tumor-bearing hind limb was shielded with lead. A single dose of 20 Gray (Gy) was delivered using a Phillips orthovoltage X-ray generator operating at 250 kV and 15 mA.
Sample_growth_protocol_ch1	B16F1 murine melanoma cells were obtained from the American Type Culture Collection (Manassas, VA) and cultured in RPMI 1640 culture medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (Atlanta Biologicals, Lawrenceville, GA), 100 units/ml penicillin and 100 mg/ml streptomycin (Invitrogen, Carlsbad, CA). Cell cultures were maintained at 37 deg C in a humidified environment containing 5% CO2. C57BL/6-NCr (C57BL/6 wild-type) mice were obtained from FCRI-Taconic (Germantown, NY). B6;129S-Tnfrsf1a[tm1Imx] Tnfrsf1b[tm1Imx]/J (TNFR1,2 -/-) breeding pairs were obtained from Jackson Laboratories (Bar Harbor, ME). Mice were 8-12 weeks of age when experimentation began. B16F1 cells (2x10^6 cells in 100 μl of phosphate-buffered saline) were injected subcutaneously into the right hind limbs of five to seven C57BL/6 and TNFR1,2 -/- mice. Tumor volume was determined by direct measurement with calipers and calculated by using the formula (length x width x depth/2). Tumors were permitted to grow to a volume of 268-478 mm3 after which mice were divided into treatment groups with equal mean tumor volumes.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	At the conclusion of each experiment, the animals were euthanized using CO2 followed by cervical dislocation in accordance with institutional guidelines. Tumors were excised five hours following treatment and snap frozen in liquid nitrogen. TRIzol extraction of total RNA was performed according to the manufacturer's instructions. Samples were pooled based on total RNA and analyzed in duplicate.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix GeneChip® Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Agilent GeneArray Scanner.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 800.
Sample_platform_id	GPL1261
Sample_contact_name	Sean,Pravin,Pitroda
Sample_contact_email	spitroda@uchicago.edu
Sample_contact_department	Radiation and Cellular Oncology
Sample_contact_institute	The University of Chicago
Sample_contact_address	5841 South Maryland Avenue, MC 1105
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60637
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM567nnn/GSM567580/suppl/GSM567580.CEL.gz
Sample_series_id	GSE23002
Sample_data_row_count	45101

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